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jlec 12/06/28 16:48:39 |
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|
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Added: hmmer-3.0-perl-5.16-2.patch |
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Log: |
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next patch |
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Revision Changes Path |
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1.1 sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch |
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch?rev=1.1&view=markup |
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plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/hmmer/files/hmmer-3.0-perl-5.16-2.patch?rev=1.1&content-type=text/plain |
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|
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Index: hmmer-3.0-perl-5.16-2.patch |
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=================================================================== |
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easel/devkit/autodoc | 4 ++-- |
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easel/devkit/esl-dependencies | 4 ++-- |
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easel/devkit/sqc | 7 +++---- |
| 18 |
easel/testsuite/coverage_report.pl | 4 ++-- |
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easel/testsuite/driver_report.pl | 4 ++-- |
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easel/testsuite/valgrind_report.pl | 4 ++-- |
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profmark/rocplot.pl | 4 ++-- |
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7 files changed, 15 insertions(+), 16 deletions(-) |
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|
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diff --git a/easel/devkit/autodoc b/easel/devkit/autodoc |
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index 16bda4d..f5c5efc 100755 |
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--- a/easel/devkit/autodoc |
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+++ b/easel/devkit/autodoc |
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@@ -49,8 +49,8 @@ |
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# |
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# SRE, Tue Nov 30 19:43:47 2004 |
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|
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-require "getopts.pl"; |
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-&Getopts('n:t'); |
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+use Getopt::Std; |
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+getopts('n:t'); |
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$cfile = shift; |
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|
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if ($opt_t) { $show_api_table = 1; } |
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diff --git a/easel/devkit/esl-dependencies b/easel/devkit/esl-dependencies |
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index a4dc126..b61fa7a 100755 |
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--- a/easel/devkit/esl-dependencies |
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+++ b/easel/devkit/esl-dependencies |
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@@ -13,8 +13,8 @@ |
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# SRE, Mon Jun 11 11:15:31 2007 |
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# SVN $Id$ |
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|
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-require "getopts.pl" |
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-&Getopts('1afr'); |
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+use Getopt::Std; |
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+getopts('1afr'); |
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|
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if ($opt_1) { $show_summary_table = 1; } |
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if ($opt_a) { $list_augfiles = 1; } |
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diff --git a/easel/devkit/sqc b/easel/devkit/sqc |
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index af3adf6..0cdb458 100755 |
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--- a/easel/devkit/sqc |
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+++ b/easel/devkit/sqc |
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@@ -205,12 +205,11 @@ |
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# SRE, Tue Aug 6 11:16:39 2002 |
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# SVN $Id: sqc 1796 2007-01-03 22:36:44Z eddys $ |
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|
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-require "getopts.pl"; |
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-require "importenv.pl"; |
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+use Getopt::Std; |
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|
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# Parse our command line |
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# |
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-&Getopts('v'); |
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+getopts('v'); |
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if ($opt_v) { $verbose = 1; } |
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|
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|
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@@ -609,7 +608,7 @@ sub check_valgrind_status |
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# |
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sub tempname { |
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my ($dir, $name, $suffix); |
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- if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";} |
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+ if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";} |
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|
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foreach $suffix ("aa".."zz") { |
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$name = "$dir"."esltmp".$suffix.$$; |
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diff --git a/easel/testsuite/coverage_report.pl b/easel/testsuite/coverage_report.pl |
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old mode 100755 |
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new mode 100644 |
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index 9c77791..024ed34 |
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--- a/easel/testsuite/coverage_report.pl |
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+++ b/easel/testsuite/coverage_report.pl |
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@@ -16,9 +16,9 @@ |
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# |
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# SRE, Thu Mar 1 19:22:57 2007 (Janelia) |
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# SVN $Id: coverage_report.pl 231 2008-03-25 14:43:57Z eddys $ |
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-require "getopts.pl"; |
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+use Getopt::Std; |
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$have_sloccount = 1; |
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-&Getopts('cs'); |
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+getopts('cs'); |
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if ($opt_c) { $do_recompile = 1; } |
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if ($opt_s) { $have_sloccount = 0; } |
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|
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diff --git a/easel/testsuite/driver_report.pl b/easel/testsuite/driver_report.pl |
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index 757854d..a9a8902 100755 |
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--- a/easel/testsuite/driver_report.pl |
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+++ b/easel/testsuite/driver_report.pl |
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@@ -25,8 +25,8 @@ |
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# SRE, Fri Mar 2 10:01:44 2007 (Janelia) |
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# SVN $Id: driver_report.pl 326 2009-02-28 15:49:07Z eddys $ |
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|
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-require "getopts.pl"; |
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-&Getopts('c'); |
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+use Getopt::Std; |
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+getopts('c'); |
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if ($opt_c) { $do_recompile = 1; } |
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|
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if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; } |
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diff --git a/easel/testsuite/valgrind_report.pl b/easel/testsuite/valgrind_report.pl |
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old mode 100755 |
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new mode 100644 |
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index 186a392..07026a0 |
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--- a/easel/testsuite/valgrind_report.pl |
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+++ b/easel/testsuite/valgrind_report.pl |
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@@ -10,8 +10,8 @@ |
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# |
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# SRE, Fri Mar 2 08:37:48 2007 [Janelia] |
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# SVN $Id: valgrind_report.pl 231 2008-03-25 14:43:57Z eddys $ |
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-require "getopts.pl"; |
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-&Getopts('c'); |
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+use Getopt::Std; |
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+getopts('c'); |
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if ($opt_c) { $do_recompile = 1; } |
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|
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if ($ENV{'CC'} ne "") { $CC = $ENV{'CC'}; } else { $CC = "gcc"; } |
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diff --git a/profmark/rocplot.pl b/profmark/rocplot.pl |
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index d4c0f67..4e8175a 100755 |
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--- a/profmark/rocplot.pl |
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+++ b/profmark/rocplot.pl |
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@@ -2,8 +2,8 @@ |
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|
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$nsearches = 1567; |
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|
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-require "getopts.pl"; |
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-&Getopts('n:X:x:'); |
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+use Getopt::Std |
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+getopts('n:X:x:'); |
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|
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if ($opt_n) { $nsearches = $opt_n; } |
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if ($opt_X) { |
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